When we think of reefs we tend to think of only one type – hard-coral. Throughout the tropics and beyond, however, there are diverse and fertile reef systems growing on black sands, or near the entrance to rivers, which harbour an incredible diversity of wildlife. These look very different. They often have a broader mix of soft corals, encrusting corals, anemones and seagrass. In this blog I want to introduce you to the wonderful world of fertile sand coral reefs. These are among my most favourite places to snorkel and dive, because of the incredible animals you find there. As we’ll find out, they are just as worthy of protection as traditional coral reefs.
I’m going to talk about three different places I know. The last of these is in Melbourne’s Port Phillip Bay. As you’ll see it’s surprisingly similar and a significant and poorly-conserved habitat, despite its importance. The other two are in the Coral Triangle. This just goes to show that there are equivalent environments in surprising places.
Three contrasting examples of fertile sand coral reefs
The first site we’ll explore is the Lembeh Strait in Indonesia. This is possibly the most famous place in the world for what is colloquially referred to as ‘muck’ diving. It is in fact, a productive and vibrant array of reefs and black sand, brilliant for both snorkelling and diving. This supports a cast of the most weird and wonderful creatures like the Hairy Frogfish, Mimic Octopus and Lembeh Sea Dragon.

The second is the entrance to the Waigeo Lagoon in Raja Ampat. Raja Ampat is the centre of the Coral Triangle, a place with three-quarters of the world’s hard corals in an area 10% of the size of the Great Barrier Reef. Inside this system, however, there are places virtually unexplored which may be more fragile and just as important as the more popularised and protected reefs.

The third is in my own backyard. Beaumaris Bay in northern Port Phillip Bay, Melbourne, is an unassuming location overlooked in preference for the reefs of Ricketts Point Marine Park. Beaumaris Bay supports an array of creatures found nowhere else in the north of the bay. It’s becoming a favourite place for me to visit and shares characteristics with the sites above, despite being a temperate reef location.

1. The Lembeh Strait – Volcanic Sand
Lembeh has become synonymous with ‘muck diving’, a misnomer that gives the impression of a barren wasteland. This couldn’t be further from the truth – in fact, this area is fantastic for both snorkelling and diving. The site is beholden to two recently active volcanoes and the black sand they create is highly fertile.
Traditional reefs are like rainforest. Sure, the number of species in rainforest is bewildering but how much wildlife do you see, compared say, to the plains of Africa? Lembeh is more akin to the fertile plains of Africa. The substrate is full of natural nutrientsEnergy and nutrients are the same thing. Plants capture energy from the Sun and store it in chemicals, via the process of photosynthesis. The excess greenery and waste that plants create, contain chemicals that animals can eat, in order to build their own bodies and reproduce. When a chemical is used this way, we call it a nutrient. As we More and the sand is soft in places. This makes it a more dynamic habitat and the animals are hiding in plain sight.
Where you might disregard the place as a desert of black sand, the animal biomassThe weight of living organisms. Biomass can be measured in relation to the amount of carbon, the dry weight (with all moisture removed) or living weight. In general it can be used to describe the volume of energy that is contained inside systems, as the size of animals relates to their metabolism and therefore, how much energy they contain and More on or just below the surface is huge. These systems are incredibly important and a joy to explore.
Fortunately, situated between mainland Sulawesi and Lembeh Island itself, the fragile sediment is relatively protected. Rather than nutrients being released fast, they slowly seep out of the volcanic black sand. Quick enough to allow grazing by a myriad of creatures and slow enough to avoid becoming eutrophicated (which means, an overabundance of nutrientA substance that contains the raw materials for life. At a chemical level, these are contained inside compounds that are absorbed into the body and essential energy-containing molecules are extracted, so that energy can be transformed into other chemical processes that use the energy for living. More, that collapses ecosystemsHow ecosystems function An ecosystem is a community of lifeforms that interact in such an optimal way that how ecosystems function best, is when all components (including humans and other animals) can persist and live alongside each other for the longest time possible. Ecosystems are fuelled by the energy created by plants (primary producers) that convert the Sun's heat energy More).

Which means Lembeh not only has vibrant, healthy and diverse coral reef at its edges but an extraordinary diversity of sea creatures below.
The number and variety of animal life is truly mind blowing. In 2-3 days we clocked up the kind of sightings we’d be happy for in two weeks in a place like Komodo, Bali or Raja Ampat.
2. Waigeo Lagoon – River Sediment
Volcanoes are one way that nutrients can be swept onto tropical reef areas. The other way is via rivers. Waigeo is a huge island in Raja Ampat, one of the ‘Four Kings’ that gives the regency its name.

In the centre of Waigeo is a lagoon that’s 30km long and 300 square kilometres in area. At its northern end it is made up of dense mangroves but it widens into an inland sea. Much of the island’s surrounding limestone mountains, creeks and rivers, empty their freshwater into the lagoon. The southern end is tidal, so the Pacific Ocean water enters on each cycle, barely mixing with the freshwater and forcing any nutrients from inside the lagoon, to fall to the seafloor. This creates very silty and nutrient-rich sediment.
We visited this location in 2023 on board Pindito. This was the first time in the ship’s 32 year history that they’d done that. We anchored just inside the narrow bay entrance and took the zodiacs about 10km north into the lagoon’s centre. What we found was quite remarkable.
Here is an extract from our trip report:
Both here and near the entrance of the lagoon were mixed coral reef, sand and seagrass. In a short time snorkelling inside we found a wealth of different creatures including sapsucking seaslugs, nudibranchs, juvenile Barramundi Cod, Chocoloate-drop Starfish and reams of Cardinalfish. Indeed, many of the common species we might see in the Lembeh Strait. Had we spent longer searching, we would have no doubt found a lot more.
Beaumaris Bay – Settlement Zone
A few thousand kilometres south is the city of Melbourne. The coastline here forms part of what’s been termed ‘the Great Southern Reef’.
Whenever water stops, settlement occurs. Port Phillip Bay is a 2,000 square kilometre inland sea. The northern two-thirds is cut off from the ocean by a line of sand banks and the narrow entrance to Bass Strait. This means that for the most part, sediment that enters the north can stay there for over 200 days before it has the chance to be flushed out to sea – plenty of time for nutrients to settle.

A slow clockwise circulation of surface water in the Bay is driven by winds and the Beaumaris Bay headland causes the currents to slow down and loop back. Like on the inside margins of a river bend, this means sediment is deposited. Hence the substrate here is quite silty and nutrient rich.
Once again, the wildlife and natural processes here are quite unique. Interestingly, for a site so far south, it harbours a number of species similar to the tropical locations above: seahorses, pipefish, sapsucking seaslugs, Blue-ringed Octopus, dragonets, snake-eels and nudibranchs. There are also fish like Little Gurnard that bear striking resemblance to the waspfishes of the tropics.
The reef here is dominated by Green Coral but the mixture of bare sediment, reef and seagrass, is often mistaken for something unnatural or insignificant. As a consequence, these habitatsWhat is habitat for animals and people? Habitat, hence the word "habitable" describes the natural surroundings in which any animal (or human) lives, that houses basic needs, such as food and shelter. Vegetation, for example, is habitat for animals. On its own, habitat is not necessarily stable or sustainable, which is why it differs from an ecosystem. Habitat in disrepair More are not conserved, unlike the more conventional-looking reefs nearby. Yet like their tropical equivalents, they are just as important and fragile, warranting more protection.
What makes fertile sand coral reefs fragile?
Nutrient in excess kills ecosystems. So what makes such high nutrient systems naturally sustainable and diverse? The answer is in the images above – wildlife. The nutrients are locked into sediment processes by animals. In most places, the gradual deposition has happened in synchrony with the gradual build-up of life. On land, this is often the norm. Most of our living environment is highly fertile and depends on animals to maintain the natural processes. Creatures ingest and recycle the nutrients back into the substrate, keeping the system in balance.
This wonderful world of fertile sand coral reefs does, however, tend to be in areas where there is a naturally high level of human activity. For example, this is the case for most river mouths, estuaries and lagoons. At the same time, they don’t look as pretty. So we presume they are barren, and miss the world of wildlife they support. These habitats may be far more threatened than the reefs we usually covet.
Next time you’re snorkelling in these areas, slow down and pay attention as you might see one of the weird and wonderful creatures that live there. You might also better understand why the wonderful world of fertile sand coral reefs is worth protecting.